utils¶
Collection of utility functions.
-
pysmFISH.utils.add_coords_to_yaml(folder, hyb_nr, hyb_key='Hyb')[source]¶ Read tile number and coordinates and add them to the yaml file. Read the tile number and microscope coordinates for each tile from the microscope file called “coord_file_name” in “folder”. Then insert them in dictionary “TilesPositions” in the yaml metadata file called Experimental_metadata.yaml.
- folder: str
- Exact path to the folder, including trailing “/”
- hyb_nr: int
- Hybridization number denoting for which hybridization we should read and insert the coordinates
- hyb_key: str
- Possible values ‘Hyb’ or ‘Strip’. To add coordinates for stripping if necessary.
-
pysmFISH.utils.check_trailing_slash(dir_path, os_windows)[source]¶ This function check if there is a trailing slash at the end of a directory path and add it if missing
- dir_path= str
- Path to the directory
- dir_path= str
- Path to the directory
-
pysmFISH.utils.combine_gene_pos(hybridizations_infos, converted_positions, hybridization)[source]¶ Gather info about the imaging at each hybridization.
This function creates a dictionary where for each hybridization are shown the genes and number of positions imaged for each gene. This function will be useful to created distribution lists for running parallel processing of the datasets.
- hybridizations_infos: dict
- Dictionary with parsed Hybridizations metadata
- converted_positions: dict
- Dictionary with the coords of the images for all hybridization. The coords are a list of floats
- hybridization: str
- Selected hybridization to process
- genes_and_positions: dict
- Dictionary where for each hybridization, the genes and number of positions imaged for each gene are showed.
-
pysmFISH.utils.create_single_directory(hyb_dir, gene, hybridization, processing_hyb, suffix, add_slash, analysis_name=None)[source]¶ Function used to create a subdirectory
- hyb_dir: str
- Path to the directory of the hybridization currently processed.
- gene: str
- Gene name to be included in the directory.
- processing_hyb: str
- Name of the hybridization processed (ex. ‘EXP-17-BP3597_hyb2’).
- suffix: str
- Extra info to add to the directory name (ex. blended).
- add_slash: str
- Slash added according to the os.
- analysis_name: str
- Name of the analysis associated to the folder
- sufx_dir_path: str
- Path to the created directory
-
pysmFISH.utils.create_subdirectory_tree(hyb_dir, hybridization, hybridizations_infos, processing_hyb, suffix, add_slash, skip_tags=None, skip_genes=None, analysis_name=None)[source]¶ Function that creates the directory tree where to save the temporary data.
- hyb_dir: str
- Path of the hyb to process
- hybridization: str
- Name of the hybridization to process (ex. Hybridization2)
- hybridizations_infos: dict
- Dictionary containing the hybridizations info parsed from the Experimental_metadata.yaml file
- processing_hyb: str
- Name of the processing experiment (ex. EXP-17-BP3597_hyb2)
- suffix: str
- Suffix to add to the folder with useful description (ex. tmp)
- add_slash: str
- ‘’ for win and ‘/’ for linux
- skip_tags: list
- tags that won’t be processed (ex. _IF)
- skip_genes list
- list of genes to skip
- analysis_name: str
- Name of the analysis run
- sufx_dir_path: str
- Path of the sufx directory of the processed hybridization
- sufx_gene_dirs: list
- List of the paths of the sufx directory for the genes to process
-
pysmFISH.utils.determine_os()[source]¶ This function check if the system is running windows. and return the correct slash type to use
- os_windows: bool
- True if the os is windows.
- add_slash: str
- ‘’ for windows or ‘/’ for any other system
-
pysmFISH.utils.experimental_metadata_parser(hyb_dir)[source]¶ Parse the yaml file containing all the metadata of the experiment
The file must be located inside the experimental folder.
- hyb_dir: str
- Path to the .yaml file containing the metadata of the experiment
- experiment_infos: dict
- Dictionary with the information on the experiment.
- HybridizationInfos: dict
- Dictionary with the information on the hybridization.
- converted_positions: dict
- Dictionary with the coords of the images for all hybridization. The coords are a list of floats
- microscope_parameters: dict
- Dictionary with the microscope parameters for all hybridization
-
pysmFISH.utils.filtering_raw_counting_config_parser(hyb_dir)[source]¶ Parse the yaml file containing all configurations for running the analysis
The file must be located inside the experimental folder.
- hyb_dir: str
- Path to the .yaml file containing the metadata of the experiment
- config_parameters: dict
- Dictionary with all the configuration parameters
-
pysmFISH.utils.general_yaml_parser(file_path)[source]¶ Parse a general yaml file and return the dictionary with all the content
The file must be located inside the experimental folder.
- file_path: str
- Path to the .yaml file containing the metadata of the experiment
- parameters: dict
- Dictionary with all the configuration parameters
-
pysmFISH.utils.identify_nodes(client)[source]¶ Function used to determine the address of the nodes in order to better split the work
- client: dask.obj
- Dask.distributed client.
- node_addresses: OrderedDict
- Ordered dictionary. The keys are the addresses of the nodes and the items are the full addresses of teh workers of a specific node.
-
pysmFISH.utils.init_console_logger()[source]¶ Send the logging output to the stderr stream. After running this function the logging message will typically end up in your console output.
-
pysmFISH.utils.init_file_logger(log_path, maxBytes=0, backupCount=0)[source]¶ Send the logging output to a file.
The logs are placed in a directory called “logs”, if this directory is not found at the location denoted by log_path, it will be made. On each run of the program a new log file will be produced. max_bytes and backup_count are passed to RotatingFileHandler directly. So a new file will be produced when the filesize reaches max_bytes. If either of max_bytes or backup_count is zero, rollover never occurs and everything will be logged in one file.
- log_path: str
- Full path to the directory where the log directory is/should go.
- maxBytes: int
- Maximum size in bytes of a single log file, a new log file will be started when this size is reached. If zero, all logging will be written to one file. (Default: 0)
- backup_count: int
- The maxinum number of logging file that will be produced. If zero, all logging will be written to one file. (Default: 0)